MolNFT v1 · #49365 · protein
Crystal structure of the heterotrimer core of the S. cerevisiae ampk homolog SNF1
2QLV · Carbon catabolite derepressing protein kinase: “Crystal structure of the heterotrimer core of the S. cerevisiae ampk homolog SNF1”. X-ray diffraction, 20 pockets (best druggability 0.86). MolNFT v1 #49365 on GenesisL1: 3D structure…
- PDB
- 2QLV
- Type
- protein
- Length
- 1,181 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbon catabolite derepressing protein kinase; Protein SIP2; Nuclear protein SNF4
- EC
- 2.7.11.1
- UniProt
- P06782, P34164, P12904
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Carbon catabolite derepressing protein kinase (EC 2.7.11.1) | protein | 133 | 39% helix, 26% strand | P06782 |
| B | Protein SIP2 | protein | 155 | 11% helix, 43% strand | P34164 |
| C, F | Nuclear protein SNF4 | protein | 310 | 41% helix, 21% strand | P12904 |
| E | Protein SIP2 | protein | 140 | 2% helix, 49% strand | P34164 |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.86 | 0.88 | 96 | empty |
| 2 | 806 | 0.84 | 0.87 | 91 | empty |
| 3 | 77 | 0.70 | 0.94 | 17 | empty |
| 4 | 80 | 0.70 | 0.94 | 18 | empty |
| 5 | 233 | 0.69 | 0.86 | 35 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1888 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1696 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1665 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 1661 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1481 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 2QLV · Crystal structure of the heterotrimer core of the S. cerevisiae AMPK homolog SNF1 · the same entry in another collection · chain F against F, TM-score 1.00
- P12904 · AlphaFold monomer V2.0 prediction for 5'-AMP-activated protein kinase subunit gamma… · a predicted model of the same protein · chain C against A, TM-score 0.96
- P06782 · AlphaFold monomer V2.0 prediction for carbon catabolite-derepressing protein kinase… · a predicted model of the same protein · chain A against A, TM-score 0.67
- P34164 · AlphaFold monomer V2.0 prediction for SNF1 protein kinase subunit beta-2 (P34164) · a predicted model of the same protein · chain E against A, TM-score 0.64
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P06782
- Every structure of UniProt P34164
- Every structure of UniProt P12904
- Elsewhere: RCSB PDB 2QLV · PDBe 2QLV · UniProt P06782 · UniProt P34164 · UniProt P12904
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